coot-data fix

10 files changed, 26 insertions, 140 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 454e31eaf..8055eb9a1 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,18 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.6.0031 (28 Apr 2009)
+*refmac-5.5.0091 (28 Apr 2009)
+
+  28 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -files/5.5.0088-allow-dynamic-linking.patch,
+  -files/5.5.0089-allow-dynamic-linking.patch,
+  -files/5.6.0030-allow-dynamic-linking.patch,
+  +files/5.6.0031-allow-dynamic-linking.patch, -refmac-5.5.0088.ebuild,
+  -refmac-5.5.0089.ebuild, +refmac-5.5.0091.ebuild, -refmac-5.6.0030.ebuild,
+  +refmac-5.6.0031.ebuild:
+  version bumps to latest and clean up of old versions
+
 *refmac-5.6.0027 (26 Apr 2009)
 
   26 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/files/5.5.0089-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0089-allow-dynamic-linking.patch
deleted file mode 100644
index 415ba9d08..000000000
--- a/sci-chemistry/refmac/files/5.5.0089-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,66 +0,0 @@
---- makefile_refmac.inc1.orig	2008-08-01 22:17:14.000000000 -0700
-+++ makefile_refmac.inc1	2008-08-01 22:18:46.000000000 -0700
-@@ -69,9 +69,7 @@
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o                    
- #$(LLIBCCP)                  \
- #crt0.o                      \
- 
-@@ -95,8 +93,7 @@
- emin.o                      \
- libcheck_min.o              \
- mol2_file.o                 \
--sdf_files.o                 \
--$(LLIBCCP)
-+sdf_files.o                 
- 
- SUBM =                      \
- main_makecif.o              \
-@@ -116,9 +113,7 @@
- make_PDB.o                  \
- makecif.o                   \
- make_unix_ccp4.o            \
--make_vdw.o                  \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+make_vdw.o                  
- 
- SUBT =                      \
- tlsgroups.o                 \
-@@ -142,9 +137,7 @@
- inout_routines.o            \
- errwrt_1.o                  \
- linalgebra.o                \
--subnumrec.o                 \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+subnumrec.o                 
- #--------------------------------------------------------------------------------
- 
- ed = echo 'g/^CMDW-5.0/s//        /@w@q@' | tr "@" "\012" | ed -s
-@@ -154,16 +147,16 @@
- all:	refmac libcheck makecif
- 
- refmac:	$(SUBR)
--	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP)
- 
- makecif:	$(SUBM)
--	$(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF)
- 
- tlsgroups:	$(SUBT)
--	$(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF)
- 
- clean:
- 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.5.0090-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0090-allow-dynamic-linking.patch
deleted file mode 100644
index 415ba9d08..000000000
--- a/sci-chemistry/refmac/files/5.5.0090-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,66 +0,0 @@
---- makefile_refmac.inc1.orig	2008-08-01 22:17:14.000000000 -0700
-+++ makefile_refmac.inc1	2008-08-01 22:18:46.000000000 -0700
-@@ -69,9 +69,7 @@
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o                    
- #$(LLIBCCP)                  \
- #crt0.o                      \
- 
-@@ -95,8 +93,7 @@
- emin.o                      \
- libcheck_min.o              \
- mol2_file.o                 \
--sdf_files.o                 \
--$(LLIBCCP)
-+sdf_files.o                 
- 
- SUBM =                      \
- main_makecif.o              \
-@@ -116,9 +113,7 @@
- make_PDB.o                  \
- makecif.o                   \
- make_unix_ccp4.o            \
--make_vdw.o                  \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+make_vdw.o                  
- 
- SUBT =                      \
- tlsgroups.o                 \
-@@ -142,9 +137,7 @@
- inout_routines.o            \
- errwrt_1.o                  \
- linalgebra.o                \
--subnumrec.o                 \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+subnumrec.o                 
- #--------------------------------------------------------------------------------
- 
- ed = echo 'g/^CMDW-5.0/s//        /@w@q@' | tr "@" "\012" | ed -s
-@@ -154,16 +147,16 @@
- all:	refmac libcheck makecif
- 
- refmac:	$(SUBR)
--	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP)
- 
- makecif:	$(SUBM)
--	$(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF)
- 
- tlsgroups:	$(SUBT)
--	$(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF)
- 
- clean:
- 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.5.0088-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0091-allow-dynamic-linking.patch
index 415ba9d08..415ba9d08 100644
--- a/sci-chemistry/refmac/files/5.5.0088-allow-dynamic-linking.patch
+++ b/sci-chemistry/refmac/files/5.5.0091-allow-dynamic-linking.patch
diff --git a/sci-chemistry/refmac/files/5.6.0030-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0031-allow-dynamic-linking.patch
index c67921eab..c67921eab 100644
--- a/sci-chemistry/refmac/files/5.6.0030-allow-dynamic-linking.patch
+++ b/sci-chemistry/refmac/files/5.6.0031-allow-dynamic-linking.patch
diff --git a/sci-chemistry/refmac/refmac-5.5.0088.ebuild b/sci-chemistry/refmac/refmac-5.5.0091.ebuild
index d53653bdc..d53653bdc 100644
--- a/sci-chemistry/refmac/refmac-5.5.0088.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0091.ebuild
diff --git a/sci-chemistry/refmac/refmac-5.5.0089.ebuild b/sci-chemistry/refmac/refmac-5.6.0031.ebuild
index d53653bdc..43f92ed20 100644
--- a/sci-chemistry/refmac/refmac-5.5.0089.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0031.ebuild
@@ -6,7 +6,7 @@ inherit eutils fortran toolchain-funcs
 
 DESCRIPTION="Macromolecular crystallographic refinement program"
 HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/"
-SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz"
+SRC_URI="${HOMEPAGE}data/refmac_experimental/${PN}_source_v${PV}.tar.gz"
 LICENSE="ccp4"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
@@ -14,7 +14,7 @@ IUSE=""
 RESTRICT="mirror"
 RDEPEND="virtual/lapack
 	virtual/blas
-	sci-libs/ccp4-libs"
+	>=sci-libs/ccp4-libs-6.1.1-r1"
 DEPEND="${RDEPEND}"
 S="${WORKDIR}"
 
@@ -39,9 +39,9 @@ src_compile() {
 }
 
 src_install() {
-	for i in refmac libcheck makecif; do
+	for i in refmac libcheck; do
 		dobin ${i} || die
 	done
 	dosym refmac /usr/bin/refmac5 || die
-	dodoc refmac_keywords.pdf || die
+#	dodoc refmac_keywords.pdf || die
 }
diff --git a/sci-libs/coot-data/ChangeLog b/sci-libs/coot-data/ChangeLog
index 4963f7b80..9f8120ad1 100644
--- a/sci-libs/coot-data/ChangeLog
+++ b/sci-libs/coot-data/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/coot-data
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/coot-data/ChangeLog,v 1.7 2009/02/23 05:51:17 darkside Exp $
+# $Header: $
+
+*coot-data-2-r1 (28 Apr 2009)
+
+  28 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +coot-data-2-r1.ebuild, -coot-data-2.ebuild:
+  fixed COOT_REFMAC_LIB_DIR
 
 *coot-data-2 (27 Apr 2009)
 
diff --git a/sci-libs/coot-data/Manifest b/sci-libs/coot-data/Manifest
index 6b606003c..bedb2c568 100644
--- a/sci-libs/coot-data/Manifest
+++ b/sci-libs/coot-data/Manifest
@@ -1,4 +1,4 @@
 DIST reference-structures.tar.gz 6945369 RMD160 0dd9b2057cf5d6b0d060d704231aa7c5518f0b3b SHA1 796842664877ae1d71b7c64bfb0219b839325cf7 SHA256 ba0a21e1f7f9065c7dd691e784d6508edc9ffae8b31923e5def5f1cbb7108b06
-EBUILD coot-data-2.ebuild 802 RMD160 9929e26a9ba63d5c3ebc9460d3c7e88dc97c0317 SHA1 c9dbf22cd22e29d8ead2e99801215e3325077447 SHA256 df0812678adda50d33b8320cb7ffceb07ef69e0e64696fa9cb9e06ce843a1f2c
-MISC ChangeLog 1317 RMD160 cc62a88a5209b4bfc45441270ac738b504f83b40 SHA1 7deb0b8bd8fa017208cca97213108c9e9ed69d08 SHA256 bff4b0e1832700cbd83083d18f5f740bf71afc4e8c85a5f7779bf43948054f2e
+EBUILD coot-data-2-r1.ebuild 793 RMD160 ba459705ff0f1c5c28396af34ebc939563959c41 SHA1 7f191c51d185340447e0d39645a2f9c3cd17518d SHA256 2658a007e21ee3cd71b2a47e27f4844a87b1e76fb715c1fe3da0471b630bc4e0
+MISC ChangeLog 1389 RMD160 038b1db57a663ac92eaa8ddd2d055eb6d586a33f SHA1 767287fe24c6de208c38abe2293ae7ce13791d21 SHA256 219aa1f0081e60c108f6770ea5de9d6e5311b4ef8f084cce56fd39438bfab058
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-libs/coot-data/coot-data-2.ebuild b/sci-libs/coot-data/coot-data-2-r1.ebuild
index 907abb418..cb4ff6b0a 100644
--- a/sci-libs/coot-data/coot-data-2.ebuild
+++ b/sci-libs/coot-data/coot-data-2-r1.ebuild
@@ -21,7 +21,7 @@ src_install() {
 	# Coot looks in the wrong spot for the monomer library
 	# Listens to ccp4's CCP4_LIB rather than CLIBD_MON
 	cat >> "${T}"/coot <<- EOF
-	COOT_REFMAC_LIB_DIR="/usr/share/ccp4/monomers/"
+	COOT_REFMAC_LIB_DIR="/usr/share/ccp4/"
 	COOT_REF_STRUCTS="/usr/share/coot/reference-structures/"
 	EOF